Comparative transcriptome analysis of flower heterosis in two soybean F1 hybrids by RNA-seq

Background. The thyroid hormone metabolite 3-iodothyronamine (3-T1AM) is rapidly emerging as a promising compound in decreasing the heart rate and lowering the cardiac output. The aim of our study was to fully understand the molecular mechanism of 3-T1AM on cardiomyocytes and its potential targets in cardiovascular diseases. Materials and Methods. In our study, we utilized RNA-Seq to characterize the gene expression in H9C2 cells after 3-T1AM treatment. Comparative transcriptome analysis, including gene ontology, signaling pathways, disease connectivity analysis, and protein-protein interaction networks (PPI), was presented to find the critical gene function, hub genes, and related pathways. Results. A total of 1494 differently expressed genes (DEGs) were identified (192 upregulated and 1302 downregulated genes) in H9C2 cells for 3-T1AM treatment. Of these, 90 genes were associated with cardiovascular diseases. The PPI analysis indicated that 5 hub genes might be the targets of 3-T1AM. Subsequently, eight DEGs characterized using RNA-Seq were confirmed by RT-qPCR assays. Conclusions. Our study provides a comprehensive analysis of 3-T1AM on H9C2 cells and delineates a new insight into the therapeutic intervention of 3-T1AM for the cardiovascular diseases.

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Comparative transcriptome analysis of barley (Hordeum vulgare L.) glossy mutant using RNA-Seq

Revista Brasileira de Botânica ◽

10.1007/s40415-016-0328-1 ◽

2016 ◽

Vol 40 (1) ◽

pp. 247-256

Author(s):

Haiye Luan ◽

Huiquan Shen ◽

Yinghu Zhang ◽

Hui Zang ◽

Hailong Qiao ◽

...

Keyword(s):

Hordeum Vulgare ◽

Transcriptome Analysis ◽

Comparative Transcriptome ◽

Rna Seq ◽

Hordeum Vulgare L ◽

Comparative Transcriptome Analysis ◽

Glossy Mutant

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Comparative transcriptome analysis reveals conserved branching morphogenesis related genes involved in chamber formation of catfish swimbladder

Physiological Genomics ◽

10.1152/physiolgenomics.00089.2017 ◽

2018 ◽

Vol 50 (1) ◽

pp. 67-76 ◽

Cited By ~ 4

Author(s):

Yujia Yang ◽

Qiang Fu ◽

Yang Liu ◽

Xiaozhu Wang ◽

Rex Dunham ◽

...

Keyword(s):

Signaling Pathway ◽

Transcriptome Analysis ◽

Channel Catfish ◽

Branching Morphogenesis ◽

F1 Hybrids ◽

Posterior Chamber ◽

Comparative Transcriptome ◽

Blue Catfish ◽

Comparative Transcriptome Analysis ◽

Hybrid Catfish

The swimbladder is an internal gas-filled organ in teleosts. Its major function is to regulate buoyancy. The swimbladder exhibits great variation in size, shape, and number of compartments or chambers among teleosts. However, genomic control of swimbladder variation is unknown. Channel catfish ( Ictalurus punctatus), blue catfish ( Ictalurus furcatus), and their F1 hybrids of female channel catfish × male blue catfish (C × B hybrid catfish) provide a good model in which to investigate the swimbladder morphology, because channel catfish possess a single-chambered swimbladder, whereas blue catfish possess a bichambered swimbladder; C × B hybrid catfish possess a bichambered swimbladder but with a significantly reduced posterior chamber. Here we determined the transcriptional profiles of swimbladder from channel catfish, blue catfish, and C × B hybrid catfish. We examined their transcriptomes at both the fingerling and adult stages. Through comparative transcriptome analysis, ~4,000 differentially expressed genes (DEGs) were identified. Among these DEGs, members of the Wnt signaling pathway ( wnt1, wnt2, nfatc1, rac2), Hedgehog signaling pathway ( shh), and growth factors ( fgf10, igf-1) were identified. As these genes were known to be important for branching morphogenesis of mammalian lung and of mammary glands, their association with budding of the posterior chamber primordium and progressive development of bichambered swimbladder in fish suggest that these branching morphogenesis-related genes and their functions in branching are evolutionarily conserved across a broad spectrum of species.

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RNA-seq-based comparative transcriptome analysis of the syngas-utilizing bacterium Clostridium ljungdahlii DSM 13528 grown autotrophically and heterotrophically

Molecular BioSystems ◽

10.1039/c3mb70232d ◽

2013 ◽

Vol 9 (11) ◽

pp. 2775 ◽

Cited By ~ 31

Author(s):

Yang Tan ◽

Juanjuan Liu ◽

Xiaohua Chen ◽

Huajun Zheng ◽

Fuli Li

Keyword(s):

Transcriptome Analysis ◽

Comparative Transcriptome ◽

Rna Seq ◽

Comparative Transcriptome Analysis ◽

Clostridium Ljungdahlii

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Comparative transcriptome analysis reveals novel insights into transcriptional responses to phosphorus starvation in oil palm (Elaeis guineensis) root

BMC Genomic Data ◽

10.1186/s12863-021-00962-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Sze-Ling Kong ◽

Siti Nor Akmar Abdullah ◽

Chai-Ling Ho ◽

Mohamed Hanafi bin Musa ◽

Wan-Chin Yeap

Keyword(s):

Transcriptome Analysis ◽

Oil Palm ◽

Crop Improvement ◽

Molecular Response ◽

Comparative Transcriptome ◽

Rna Seq ◽

Response Mechanism ◽

Transcriptional Responses ◽

Comparative Transcriptome Analysis ◽

Pi Deficiency

Abstract Background Phosphorus (P), in its orthophosphate form (Pi) is an essential macronutrient for oil palm early growth development in which Pi deficiency could later on be reflected in lower biomass production. Application of phosphate rock, a non-renewable resource has been the common practice to increase Pi accessibility and maintain crop productivity in Malaysia. However, high fixation rate of Pi in the native acidic tropical soils has led to excessive utilization of P fertilizers. This has caused serious environmental pollutions and cost increment. Even so, the Pi deficiency response mechanism in oil palm as one of the basic prerequisites for crop improvement remains largely unknown. Results Using total RNA extracted from young roots as template, we performed a comparative transcriptome analysis on oil palm responding to 14d and 28d of Pi deprivation treatment and under adequate Pi supply. By using Illumina HiSeq4000 platform, RNA-Seq analysis was successfully conducted on 12 paired-end RNA-Seq libraries and generated more than 1.2 billion of clean reads in total. Transcript abundance estimated by fragments per kilobase per million fragments (FPKM) and differential expression analysis revealed 36 and 252 genes that are differentially regulated in Pi-starved roots at 14d and 28d, respectively. Genes possibly involved in regulating Pi homeostasis, nutrient uptake and transport, hormonal signaling and gene transcription were found among the differentially expressed genes. Conclusions Our results showed that the molecular response mechanism underlying Pi starvation in oil palm is complexed and involved multilevel regulation of various sensing and signaling components. This contribution would generate valuable genomic resources in the effort to develop oil palm planting materials that possess Pi-use efficient trait through molecular manipulation and breeding programs.

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Comparative transcriptome analysis of RNA-seq data for cold-tolerant and cold-sensitive rice genotypes under cold stress

Journal of Plant Biology ◽

10.1007/s12374-014-0183-1 ◽

2014 ◽

Vol 57 (6) ◽

pp. 337-348 ◽

Cited By ~ 37

Author(s):

Chunxiu Shen ◽

Ding Li ◽

Ronghua He ◽

Zhen Fang ◽

Yumei Xia ◽

...

Keyword(s):

Cold Stress ◽

Transcriptome Analysis ◽

Comparative Transcriptome ◽

Rna Seq ◽

Comparative Transcriptome Analysis ◽

Cold Tolerant ◽

Cold Sensitive ◽

Rice Genotypes

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Comparative transcriptome analysis of inbred lines and contrasting hybrids reveals overdominance mediate early biomass vigor in hybrid cotton

10.21203/rs.2.9665/v1 ◽

2019 ◽

Author(s):

Kashif Shahzad ◽

Xuexian Zhang ◽

Liping Guo ◽

Tingxiang Qi ◽

Huini Tang ◽

...

Keyword(s):

Circadian Rhythm ◽

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Expression Patterns ◽

F1 Hybrids ◽

Pcr Analysis ◽

Genetic Constitution ◽

Comparative Transcriptome ◽

Comparative Transcriptome Analysis ◽

Extracellular Region

Abstract Background: Heterosis breeding is the most useful method for yield increment around the globe. Heterosis is an intriguing process to develop superior offspring to either parent in the desired character. The biomass vigor produced during seedling emergence stage has a direct influence on yield heterosis in plants. Unfortunately, the genetic basis of early biomass vigor in hybrid cotton is poorly understood. Results: Three stable performing F1 hybrids varying in yield heterosis named as high, medium and low hybrids with their inbred parents were used in this study. Phenotypically, these hybrids established noticeable biomass heterosis during the early stage of seedling growth in the field. Transcriptome analysis of root and leaf revealed that hybrids showed many differentially expressed genes (DEGs) relative to their parents, while the comparison of inbred parents showed limited number of DEGs indicating similarity in their genetic constitution. Further analysis indicated that expression patterns of most DEGs were overdominant in both tissues of hybrids. According to GO results, functions of overdominance genes in leaf were enriched for chloroplast, membrane, and protein binding, whereas functions of overdominance genes in root were enriched for plasma membrane, extracellular region, and responses to stress. We found that several genes of circadian rhythm pathway related to LATE ELONGATED HYPOCOTYL (LHY) showed downregulated overdominant expressions in both tissues of hybrids. In addition to circadian rhythm, several leaf genes related to Aux/IAA regulation and many root genes involved in peroxidase activity also showed overdominant expressions in hybrids. Twelve genes involved in circadian rhythm plant were selected to perform qRT-PCR analysis to confirm the accuracy of RNA-seq results. Conclusions: Through genome-wide comparative transcriptome analysis, we strongly predict that overdominance at gene expression level plays a pivotal role in early biomass vigor of hybrids. The combinational contribution of circadian rhythm and other metabolic processes may be controlled vigorous growth in hybrids. Our result provides an important foundation for dissecting molecular mechanisms of biomass vigor in hybrid cotton.

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